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Guo Y, Hu S, Li K, Xinke T, Sun Y, Gao J. Proposal of Bacillus ciccensis Liu et al. as a Later Heterotypic Synonym of Cytobacillus solani (Liu et al.) Patel and Gupta Using Comparative Genomic Analysis. Curr Microbiol 2021; 78:843-847. [PMID: 33410954 DOI: 10.1007/s00284-020-02307-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 11/24/2020] [Indexed: 12/14/2022]
Abstract
Bacillus ciccensis and Cytobacillus solani were reported to belong to separate genomic species based on a polyphasic taxonomic approach. However, we found that type strains of B. ciccensis and C. solani should belong to the same genomic species based on the clustering patterns resulting from genome phylogenetic analysis. The average nucleotide identity and digital DNA-DNA hybridization values between the genomes of two type strains were 99.6% and 96.9%, respectively, much higher than 95 ~ 96% and 70% cut-off point proposed and generally accepted species boundary. This result was also supported by a comprehensive comparison of phenotypic characteristics between the two type strains. These results suggested that B. ciccensis and C. solani had the same taxonomic position. Consequently, we propose that B. ciccensis is a later heterotypic synonym of C. solani.
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Affiliation(s)
- Yihui Guo
- School of Life Science, Hunan University of Science and Technology, Xiangtan, 411201, China
| | - Siren Hu
- School of Life Science, Hunan University of Science and Technology, Xiangtan, 411201, China
| | - Kaiqin Li
- School of Life Science, Hunan University of Science and Technology, Xiangtan, 411201, China
| | - Tang Xinke
- School of Life Science, Hunan University of Science and Technology, Xiangtan, 411201, China
| | - Yuandong Sun
- School of Life Science, Hunan University of Science and Technology, Xiangtan, 411201, China
| | - Jian Gao
- School of Life Science, Hunan University of Science and Technology, Xiangtan, 411201, China.
- Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-Polluted Soils, College of Hunan Province, Xiangtan, 411201, China.
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Gupta RS, Patel S, Saini N, Chen S. Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for an emended genus Bacillus limiting it only to the members of the Subtilis and Cereus clades of species. Int J Syst Evol Microbiol 2020; 70:5753-5798. [PMID: 33112222 DOI: 10.1099/ijsem.0.004475] [Citation(s) in RCA: 199] [Impact Index Per Article: 49.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To clarify the evolutionary relationships and classification of Bacillus species, comprehensive phylogenomic and comparative analyses were performed on >300 Bacillus/Bacillaceae genomes. Multiple genomic-scale phylogenetic trees were initially reconstructed to identify different monophyletic clades of Bacillus species. In parallel, detailed analyses were performed on protein sequences of genomes to identify conserved signature indels (CSIs) that are specific for each of the identified clades. We show that in different reconstructed trees, most of the Bacillus species, in addition to the Subtilis and Cereus clades, consistently formed 17 novel distinct clades. Additionally, some Bacillus species reliably grouped with the genera Alkalicoccus, Caldalkalibacillus, Caldibacillus, Salibacterium and Salisediminibacterium. The distinctness of identified Bacillus species clades is independently strongly supported by 128 identified CSIs which are unique characteristics of these clades, providing reliable means for their demarcation. Based on the strong phylogenetic and molecular evidence, we are proposing that these 17 Bacillus species clades should be recognized as novel genera, with the names Alteribacter gen. nov., Ectobacillus gen. nov., Evansella gen. nov., Ferdinandcohnia gen. nov., Gottfriedia gen. nov., Heyndrickxia gen. nov., Lederbergia gen. nov., Litchfieldia gen. nov., Margalitia gen. nov., Niallia gen. nov., Priestia gen. nov., Robertmurraya gen. nov., Rossellomorea gen. nov., Schinkia gen. nov., Siminovitchia gen. nov., Sutcliffiella gen. nov. and Weizmannia gen. nov. We also propose to transfer 'Bacillus kyonggiensis' to Robertmurraya kyonggiensis sp. nov. (type strain: NB22=JCM 17569T=DSM 26768). Additionally, we report 31 CSIs that are unique characteristics of either the members of the Subtilis clade (containing the type species B. subtilis) or the Cereus clade (containing B. anthracis and B. cereus). As most Bacillus species which are not part of these two clades can now be assigned to other genera, we are proposing an emended description of the genus Bacillus to restrict it to only the members of the Subtilis and Cereus clades.
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Key Words
- classification of Bacillus species
- conserved signature indels
- emendation of genus Bacillus
- genus Bacillus and the family Bacillaceae
- novel Bacillaceae genera Alteribacter, Ectobacillus, Evansella, Ferdinandcohnia, Gottfriedia, Heyndrickxia, Lederbergia, Litchfieldia, Margalitia, Niallia, Priestia, Robertmurraya, Rossellomorea, Schinkia, Siminovitchia, Sutcliffiella and Weizmannia
- phylogenomic and comparative genomic analyses
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Affiliation(s)
- Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton L8N 3Z5, Ontario, Canada
| | - Sudip Patel
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton L8N 3Z5, Ontario, Canada
| | - Navneet Saini
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton L8N 3Z5, Ontario, Canada
| | - Shu Chen
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton L8N 3Z5, Ontario, Canada
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Zheng X, Liu G, Wang Z, Wang J, Zhang H, Liu B. Bacillus dafuensis sp. Nov., Isolated from a Forest Soil in China. Curr Microbiol 2020; 77:2049-2055. [PMID: 32382951 DOI: 10.1007/s00284-020-02014-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 04/24/2020] [Indexed: 11/29/2022]
Abstract
A Gram-staining-positive, motile, rod-shaped, aerobic bacterial strain FJAT-25496 T was isolated from a forest soil sample collected from Dafu County, Chengdu City, Sichuan Province, China. Strain FJAT-25496 T grew at 15-50 °C (optimum 35 °C), pH 6.0-10.0 (optimum 8.0), and NaCl tolerance of 0-4.0% (w/v) (optimum 0%). The strain contained iso-C15:0 and anteiso-C15:0 as the predominant cellular fatty acids as well as MK-7 as the only menaquinone. The major polar lipids were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), and phosphatidyl glycerol (PG). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain FJAT-25496 T was a member of the genus Bacillus, and most closely related to Bacillus solani FJAT-18043 T (97.8%), Bacillus praedii FJAT-25547 T (97.8%), Bacillus depressus BZ1T (97.7%), Bacillus oceanisediminis H2T (97.7%), and Bacillus ciccensis 5L6T (97.6%). Based on complete genome comparisons between strain FJAT-25496 T and the type strains of its closely related species, the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values were 73.4-76.3% and 21.7-23.2%, respectively. The genomic DNA G + C content of strain FJAT-25496 T was 36.9%. On the basis of phenotypic, phylogenetic, chemotaxonomic, and genomic features, strain FJAT-25496 T is considered to represent a novel species of the genus Bacillus, for which the name Bacillus dafuensis sp. nov. is proposed. The type strain is FJAT-25496 T (= CCTCC AB 2019182 T = KCTC 43120 T).
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Affiliation(s)
- Xuefang Zheng
- Agrobiological Resource Research Institute, Fujian Academy of Agriculture Sciences, Fuzhou, 350003, China
| | | | - Ziran Wang
- Dean of Department of Biochemistry and Biotechnology, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Jieping Wang
- Agrobiological Resource Research Institute, Fujian Academy of Agriculture Sciences, Fuzhou, 350003, China
| | - Haifeng Zhang
- Agrobiological Resource Research Institute, Fujian Academy of Agriculture Sciences, Fuzhou, 350003, China
| | - Bo Liu
- Agrobiological Resource Research Institute, Fujian Academy of Agriculture Sciences, Fuzhou, 350003, China.
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Liu Y, Yan H, Zhang X, Zhang R, Li M, Xu T, Yang F, Zheng H, Zhao J. Investigating the endophytic bacterial diversity and community structures in seeds of genetically related maize ( Zea mays L.) genotypes. 3 Biotech 2020; 10:27. [PMID: 31950006 DOI: 10.1007/s13205-019-2034-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 12/23/2019] [Indexed: 12/14/2022] Open
Abstract
This research aimed to investigate the composition and diversity of endophytic bacterial community in seeds of four hybrid maize and their parental lines, which was used to reveal the potential relationship and association of endophytic bacteria between maize genotypes and their genetic relevance. High-throughput sequencing (HTS) technology showed that a total of 1419 OTUs (46.6%) were parental lines unique and 1052 OTUs (34.5%) were hybrid varieties unique, with only 575 core OTUs revealed in all the samples. Most OTUs belonged to Proteobacteria. Enterobacter (23.2%), Shigella (21.2%), Pseudomonas (15.8%) and Achromobacter (10.1%) were the major genera; the bacterial community composition and diversity of endophytic bacteria were inconsistent among different seed genotypes. Based on principal component analysis (PCA), the results referred that the endophytic composition of hybrid sample showed obvious correlation with their female parental lines, and in 'Jingke968' and 'MC738' with the same female line the endophytic community was more similar than other hybrid samples. This was the first ever use of HTS technology for investigating the endophytic bacterial diversity and community structures in seeds of genetically related maize genotypes, it was shown that, there were core microbes shared among all genotypes of seed samples, and the female parental line was more significant to impact on the composition of their hybrid seeds than male parental line. This study would provide scientific clues for the future research on the vertical transmission of endophytes among maize generations.
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Affiliation(s)
- Yang Liu
- 1College of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083 China
| | - Hai Yan
- 1College of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083 China
| | - Xiaoxia Zhang
- 2Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Beijing, 100081 China
| | - Ruyang Zhang
- 3Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 China
| | - Miao Li
- 1College of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083 China
| | - Tianjun Xu
- 3Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 China
| | - Fuzhen Yang
- 1College of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083 China
| | - Huajun Zheng
- 4Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203 China
| | - Jiuran Zhao
- 3Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 China
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Liu Y, Yang F, Nguyen TTH, Wu X, Xu Y, Kim SG. Complete genome sequence of Bacillus ciccensis 5L6 T, a new species isolated from maize (Zea mays L.) seeds with anti-fungal activity. Microb Pathog 2019; 137:103753. [PMID: 31539588 DOI: 10.1016/j.micpath.2019.103753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/19/2019] [Accepted: 09/16/2019] [Indexed: 11/29/2022]
Abstract
Maize is a crop grown worldwide. Bacillus ciccensis 5L6T was isolated from maize (Zea mays L., Jingke968) seeds and was a new species of Bacillus with potential anti-fungal activity. The complete genome of 5L6T was sequenced and assembled with a length of 5,207,802 bp and a GC content of 37.42%. The proteins responsible for anti-fungal activity and the potential beneficial interaction with maize of 5L6Twere annotated and reported here. The complete genome sequence of the new species B. ciccensis 5L6T will promote its biological application.
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Affiliation(s)
- Yang Liu
- College of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, PR China.
| | - Fuzhen Yang
- College of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, PR China
| | - Tra T H Nguyen
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeonbuk, 56212, South Korea
| | - Xianyu Wu
- College of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, PR China
| | - Youqiang Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, 100048, PR China.
| | - Song-Gun Kim
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeonbuk, 56212, South Korea; University of Science and Technology (UST), Daejeon, 34113, South Korea.
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